Clash of the Phantoms
by Marcus S. Lazarus
Summary: -3rd in 'Phantom' trilogy- With his position in Atlantis now official, John must overcome his own perception of himself as old foes assume a new approach and his relationship with Elizabeth develops further
1. Out of the Mask

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: The third part in my 'Phantom of Atlantis' trilogy (Reading the first two stories in the series is highly recommended to ensure that you understand what's going on); for those returning fans, this take place about a month after the conclusion of 'Mystery of the Phantom', and as currently planned will cover the remaining key storylines in 'Atlantis', with some obvious and significant differences…

AN 2: Thanks are due to Elgin, who helped me refine a few details regarding the consequences of John's new role

Clash of the Phantoms

Sitting in his room as he adjusted his new suit- his complicated status meant that 'dress blues' weren't an official requirement, but General O'Neill had convinced him of the need to have something smart to wear in case a formal occasion or two came up- John was amazed that his life had gone through so many changes so quickly over the last few months.

On some level, it seemed like only yesterday that he'd still been acting as the Phantom the same way he'd done for years, hiding in the shadows and secret passages of Atlantis as he kept a careful eye on the city's inhabitants, and now he was in charge of the city's military contingent and essentially the second-in-command of the whole place. He'd been back in Atlantis for over a month now since his training on Earth had concluded, but it felt strange to have an actual room to himself rather than whatever safe location he could find in some of the city's maintenance tunnels.

With his presence in the city now public, Elizabeth had convinced him to deactivate some of the security protocols he'd established around certain parts of the city, arguing that they weren't needed now that he was there to explain _why _he'd sealed them away in the first place. Most of the rooms' contents were a surprise even to him- he'd recognised that the objects within the locked areas were dangerous when he'd found them, but he hadn't thought about most of them for so long he'd almost forgotten about them- but with the expedition's scientists to confirm his own assessment, they'd managed to dig up a few interesting pieces of technology.

The Ancients' temporary residence in the city had also opened up far more doors than even he had ever been able to access; he might have had access to several ZPMs, but he'd always restricted himself to one at a time when he was alone in the city, but the Ancients had been able to access far more buildings during their brief return. He'd had to stop McKay accidentally activating a DNA resequencing device they'd found in one area before the scientist did something serious to himself, and it had been a bit difficult to convince some of the staff not to touch that bizarre social experiment thing- it apparently resembled some kind of computer game back on Earth; he'd had to make a quick change and then take a team to the planet it was looking at to prove his claims- but once the first couple of teething troubles were out of the way even the most doubtful had accepted that he knew what he was talking about.

He'd even ensured that those new areas would stay open by providing the city with additional ZPMs from his own storage unit, as well as sending a few more back to Earth for use in the _Daedalus_ and other future ships, even if he'd taken care not to reveal just how many he had in his 'storehouse'; he wanted to keep some in reserve in case they were needed. He had also managed to neatly deflect attempts to convince him to reveal that information to the IOA and the rest of the Atlantis by claiming that he preferred to keep it quiet for reasons of security (The fact that the Wraith had already hacked the Atlantis database at least once made that far easier; he might have stopped the hack then, but it set a precedent that nobody wanted to risk repeating).

Of course, it wasn't as though there hadn't been some problems with his transition from his old role as mysterious vigilante to his new official status, but it was nothing for him to worry about. Most of the military personnel who disapproved of his presence had made their tastes clear by requesting to be transferred from Atlantis after the announcement was made, and while some of the science or medical team sometimes looked at him as though they were waiting for him to make some kind of mistake or expose his 'true intentions' (The memory of what General O'Neill had told him some people believed he'd been doing was hard to forget), in general everyone seemed willing to accept that he was only here to help, and the only thing that had changed since the old days was that he was officially allowed to do so. The new additions to his staff had also been generally welcoming. Captain Satterfield in particular had appreciated his insight into how the Wraith thought beyond a purely military perspective, and John admitted that he was coming to like her as well; her welcoming attitude made him feel like she was his younger sister in an odd way, appreciating his insight into life while still capable of handling herself.

Even without the larger problems, his appointment to the senior staff was currently somewhat problematic. Elizabeth had accepted him without hesitation, but Teyla and Ronon still looked at him as though they were waiting for the moment he'd revert to type and attack them; even if they accepted that he wasn't a traditional Wraithspawn, centuries of prejudice wasn't something that would be easily forgotten. McKay and Beckett were fairly neutral about his presence, accepting his new role even if they weren't completely comfortable with it, and Lorne and Satterfield were generally casual about it (He'd requested that they attend the meetings to provide him with the necessary military perspective and strategic intelligence he was still working on presenting, and so far they'd lived up to all his expectations).

Still, complicated personal dynamics aside, the Expedition's return to Pegasus had gone rather well. They maintained their tentative alliance with the Genii, the Athosians were willing to return to their previous roles working as local guides for recon teams, and their other major alliances had been easily re-established, particularly when their allies learned that the expedition was now officially working with the Phantom.

As far as the wider galaxy was concerned, nobody outside the expedition staff aside from a few trusted Athosians were aware that the Phantom and Atlantis's new military commander were the same person, but the knowledge that he was working with them officially was a definite boost to all relevant morale.

The Taranians had been particularly grateful to learn that contact between the Phantom and the city was now official, and their role in the daily operation of the _Orion _continued to be appreciated; Norena was essentially the ship's chief science officer, and Colonel Dixon had expressed nothing but satisfaction with her performance so far. With the recovery of the _Tria_'s database, the _Orion _crew and the expedition had managed to uncover some interesting details that it would have taken far longer to find if they were searching through Atlantis's own records.

The ships' databases hadn't provided anything particularly interesting yet- as an example, there were some brief descriptions of how to recharge the ZPMs, but there was nothing to indicate how to create them in the first place or how to assemble the necessary recharging equipment- but they had been able to direct them to a few interesting gate addresses that they wouldn't have arrived at on their own for some time.

The current destination was a planet on the outskirts of the Pegasus Galaxy, which had helped to protect it from attracting the attention of the Wraith. Unlike the expedition's less pleasant contact with Halcyon the previous year- one planet where John freely admitted that the expedition had been far better qualified to help than he had been; his status as a legend made it difficult for the Phantom to encourage social change- this world, known to its inhabitants as Rhean, had managed to develop a far more positive culture, based less around military conquest and more about improving their own world. The Ancient database from the _Tria _had identified the world as the sight of a former Ancient research outpost that had fallen victim to some kind of accident during the Wraith war that had infected most of the population with an unspecified disease, but had noted that the radiation that caused the disease would have died down by now.

When John and his new team had visited the relevant gate address, they'd learned that the planet had acquired an indigenous population that had set up a colony in most of the abandoned Ancient buildings at some point after the radiation had died down, using some of the information in the planet's database to improve their environment and ensure their safety from the Wraith.

While Rhean was far enough away from the heart of the galaxy to avoid attracting the majority of the Wraith forces in Pegasus, the Rheans were still aware of the dangers out in the wider universe, and were using the outpost's available resources to try and improve their daily lives before they tried to look further afield. The outpost had little to offer compared to Atlantis's resources, but they'd already managed to uncover some interesting terraforming systems, and had even worked out how to activate the outpost's defensive shield- a weaker version of the Atlantis shield but still fairly durable- along with a cloaking system.

Of course, the Rheans' limited population- virtually the planet's entire population lived around the outpost itself- meant that their study of the outpost had been highly publicised, with the result that Atlantis's contact with them had swiftly become a major cause for celebration on the planet as well as for the expedition. As the official announcement of the new alliance with the Rheans was the first big event that Atlantis had experienced since John Sheppard had become its military commander, it meant that his presence was required at the treaty signings and the party that was being held in their honour in the aftermath (Elizabeth was going to do most of the work, but it was still up to John to be there to supervise everything).

It might not be a completely leisurely outing, but as he finished adjusting his suit and left his room to join his team at the Stargate, John had to admit that he was kind of looking forward to this; he hadn't been to a party since before he arrived in Pegasus…

And the fact that he was going to get a chance to dance with Elizabeth was _not _the main reason for his enjoyment; the dance was just a… welcome bonus.

He'd accepted that Elizabeth would only ever see him as a friend and colleague; why couldn't he _get over it_…?

* * *

AN 3: Slow start, I know, but be patient; things will become more interesting after the next chapter…


	2. John Sheppard's First Night Out

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This chapter proved tricky at times, but I hope it was worth it; we're coming up to my interpretation of one of my favourite episodes of 'Atlantis'…

Clash of the Phantoms

Walking alongside Elizabeth as the Atlantis team were guided to the main hall, John fought down the urge to scratch at his face. The make-up used to create his 'regular appearance' was very good at feigning the appearance of regular skin, but it still felt somewhat uncomfortable against his damaged face, made worse by his inability to scratch it in case he ruined his disguise…

Still, his own discomfort was a small price to pay compared to everything else that was going on right now. The treaty signing had gone as well as could be expected, Elizabeth and the Rhean leader only needing a few moments to clarify a few of the finer details, and they were currently being escorted further into the town's main hall in order to enjoy the subsequent celebration.

"Here we are," Mayor Coralin said, smiling as he indicated the central hall before them, the walls resembling Atlantis's usual architecture apart from some slight stains and wear and tear around the corners. "Our central hall; I apologise for its relative simplicity."

"Don't worry about it," Elizabeth said, smiling at them in understanding as she glanced around the room. The decorations added to the room were relatively sparse, consisting only of a few tapestries on the walls and some basic furniture in the corners, but the stage set up at one end of the hall and the band assembled there added an extra warmth to the hall that Atlantis had never quite managed to possess even after three years (John wouldn't consider the possibility that he'd contributed to that; he'd never intended to act like an oppressive force and had no doubt that Elizabeth would have told him if he was creating a bad impression). "We've dealt with the fine print; it's time to just have some fun."

"A sentiment that I am sure my people agree with just as much, Doctor Weir," Coralin said, smiling at her once more before he waved a hand at the band at the other end of the hall. The instruments they were playing didn't immediately resemble anything John was familiar with, but as they began playing the resulting rhythm was actually rather pleasant, creating a soothing atmosphere that felt intriguing rather than confusing due to the unfamiliar notes.

As the expedition members attending the treaty signing filed into the hall, John moved over to discreetly take up a position between the door and a window, to better assess the new arrivals. The fact that the hall was so full made John more and less comfortable at the same time; on the one hand, he wasn't used to crowds after spending so long alone in Atlantis, but on the other hand, he felt less conspicuous this way, even if he was here as a high-ranking member of the Atlantis expedition.

As well as the city's senior staff and some of Atlantis's more long-term residents, Colonel Dixon and some of the other senior staff for the _Orion _had decided to attend the party as well, but the _Orion _itself was remaining in orbit; it might be capable of landing, but it was easier to leave the ship in space rather than bring it into land. Glancing over, John was pleased to see Dixon sharing a dance with Norina Pero; the Taranian scientist had proven to be a quick study once given access to more advanced resources than what the Ancients had originally left on Taranis, and even the _Orion_'s Tau'ri crewmembers were comfortable regarding her as the ship's chief scientist, as well as the unofficial leader of the Taranian section of the crew.

Atlantis's connections in Pegasus were still fairly tentative aside from their contact with the Athosians, but with Atlantis now able to officially proclaim that they were allied with the Phantom, even the IOA had to admit that John's information was proving to be very helpful in terms of improving their relationship with their allies.

As the last of the attendees entered the hall, John allowed the music to wash over him as he turned to study the view through the nearby window. The night sky he witnessed was one of the most incredible he'd ever seen, a band of stars seemingly spreading out from the planet as the rest of the Pegasus Galaxy extended away from their current location, the stars standing out all the more brightly in the absence of other light sources in this part of space.

He enjoyed his life in Atlantis, but one thing John had missed about being able to travel through the Stargate during his time in hiding was the chance to see different stars like this…

"Shall we dance?"

John had been intending to turn the offer down when he initially turned around, but when he realised that Elizabeth was the one who had made the offer, he suddenly didn't know what to say apart from nodding politely at her and taking her hand as she led him to the dancefloor.

He didn't know the song, and his knowledge of any dance routine was limited, but as he moved across the dance floor with Elizabeth in his arms, standing slightly apart even as Elizabeth's hands met behind his neck and they swayed in time with the music, John had to fight down the urge to grin like an idiot at the sensation of her body so close to his.

Even if it never went further than this moment, even if she would never be closer to him than this for anything more than the occasion hug (And that was if he was lucky), these moments with her made all the hassle he'd endured back on Earth to 'qualify' for this position more than worth the effort. To know that she could see everything he was capable of and still trust him in such close proximity…

He'd never have the relationship he wanted, but he could accept what she was willing to give him if it led to moments like this.

"You're doing well," Elizabeth said, smiling as she stepped back to look approvingly at him.

"Just following your lead…" John said, shrugging dismissively as he resisted the urge to continue the dance; feeling her body pressed against his was more than he'd ever had a right to expect, but he couldn't afford to push his luck in case he gave away any more than he wanted to. "I'm just going to… scope this area out."

"Joh, we trust these people-"

"And I'm responsible for your security as part of my new position; I have to be sure," John said defensively. With that said, he stood back and walked over to the centre of the room, solemnly assessing his surroundings and the people dancing around as the party continued.

In truth, he was already fairly confident that the place would be secure from his earlier assessment, but if he didn't get away from Elizabeth, he wasn't sure what he'd do; being able to work with her on a regular basis was torture to his self-control…

Glancing around the hall to try and take his mind off that issue, John smiled as he saw McKay and Zelenka engaged in a heated discussion despite the best efforts of their dates ( John recognised Katie Brown from the botany department, but the identity of Zelenka's partner eluded him at the moment). They might have been working in different areas for a while when the expedition was sent back to Earth, but clearly some things didn't change no matter how much time people spent apart.

Satisfied that the two scientists were having no more trouble with each other than usual, John continued to assess the room. At one point, he noticed that Teyla was sharing a dance with a Japanese woman John didn't immediately recognise- he'd seen her working in the labs, but he couldn't place the name- but before he could start wondering what that said about either woman, the Athosian had handed the Japanese woman over to Ronan, the woman's brief appearance of panic being cut short as she and Ronan began to move across the floor. John guessed that the unfamiliar woman just needed some encouragement to open up after spending so long in the lab; the expedition weren't all workaholics, but there was only so much that they could do on Atlantis at the moment.

By contrast to the scientists, Satterfield was easily fitting in with the new environment, somehow managing to look particularly fetching despite wearing a standard dress uniform no more remarkable than those sported by the rest of the female military personnel present, having a different partner for each dance as the party unfolded. Even Elizabeth only had a couple of dances at a time, otherwise sitting off to the side discussing some of the finer details with other leaders, whether other department heads from Atlantis or some of the local leaders (And no, John was _not _jealous that other people were talking to her; so long as nobody tried to pull a Lucius, Elizabeth could make her own life…).

John was aware that sitting in a corner and drinking the local equivalent of beer might not be exactly sociable, but he was keeping himself available if anyone wanted to talk; he just didn't want to distract himself from his primary mission. Major Lorne, Colonel Dixon and everyone else had come a long way to be here and deserved the chance to experience what life in Pegasus had to offer; he was so familiar with some of the finer details by now that he didn't mind missing out on the simple things to ensure that others had a good time.

"Thank _god_…" a familiar voice said as someone slumped down in the chair beside John, clearly exhausted.

"Doctor Beckett?" John said, looking at his new companion in surprise, the man clearly sweating in his unusually formal suit. "What's wrong?"

"Just… well… the mayor's assistant," Beckett said, indicating a rather fetching young woman with dark hair wearing a form-fitting dark blue dress, standing at the hall's bar and looking at the doctor in a very seductive manner. "I mean, she was nice enough when we were talking earlier, but then we started dancing, and…"

"And it went wrong?" John asked. "What, did you step on her foot or something?"

"No, that's the thing; it was all fine, but I'm just…" Beckett said, voice trailing off as he looked awkwardly at the woman before he looked back at John. "I'm just not _used _to this… kind of attention…"

"Weren't you dating Laura Cadman before you went back to Earth?"

"Yeah, but it didn't really work out; probably something to do with us having our first kiss through Rodney," Beckett said, smiling briefly at the memory before he looked anxiously at the woman. "The point is, I'm just getting out of one relationship, and now-"

"Doctor Beckett, I've… not exactly been a social guy for the last few years; if you're looking for advice on what to do in this situation, I'm far from the best person to ask," John said, looking apologetically at the other man; he appreciated that the other man was trying to bond, but this was so far out of his experience that it was ridiculous to imagine anyone thinking that he could offer useful advice right now. "All I can say is that, if you like spending time with her… well, considering how hard it is to meet people here, anything's worth giving it a shot; worry about everything else later on."

"Oh," Beckett said, apparently realising that there was something deeper about that comment, but clearly recognising that this wasn't the time to press the issue. Nodding at John in understanding, he took a quick gulp of his drink and then turned back towards the woman, the two resuming their dance a few moments later. The doctor still appeared to be somewhat awkward around his partner, but at least he was giving her a chance; in a world this complicated, it was always good to find someone.

It was just too bad that his someone would never see him that way…

Wanting to avoid that thought, John turned and headed for the nearest exterior door, slipping out before anyone could see him; after spending the last two years stuck inside places, he needed to start spending more time out in the air before he started to get too used to it. Once he was sure that nobody would follow him, John settled into position as he stared upwards, the reassuring metal at his back and the vegetation spread out before him a welcome change from past trips he'd been on recently as he resumed his earlier contemplation of the night sky.

Back when he'd been training as the Phantom, he'd sometimes left Atlantis to take a break on other worlds, exploiting the fact that he was the only one who could dial Atlantis's gate at that time, but he'd always been restricted to uninhabited planets to limit the risk of being discovered- it wouldn't have done for anyone to find the legendary Phantom _training_-; as much as he'd appreciated the chance to relax, those trips had just reinforced how fundamentally alone he had been in this part of the galaxy. Every trip had always brought home just how alone he was on his chosen path, unable to spend too much time with anyone in case they saw what was under his mask or witnessed something that would make them question the legend he was trying to create around himself; he'd been the Phantom for so many years it was an effort to just be John Sheppard at times.

Elizabeth made it easier, of course- he'd spent so long letting down his guard when talking to her now-cremated future self that he associated her with the ability to relax- but there was only so much that she could do to help _him _when a whole city depended on her for leadership…

Right now, however, with the chance to rest on a world that had other people on it without worrying too much about how people would perceive him… the opportunity to see the sky and natural vegetation on a populated world… and being able to do it all when everyone else saw him as just one of the crowd from Atlantis, rather than revering him as 'the Phantom of the Ancestors' (A title that he was going to start discouraging as soon as he could after the 'Ancestors' had turned out to be complete dicks)…

He hadn't realised how much he'd missed those simple things until he'd been to Earth…

"Excuse me?" a voice said from behind him.

Turning around, John smiled politely at the young woman coming up behind him, wearing a long dark coat over her dress.

"Are you… all right?" the woman asked, looking uncertainly at him. "The party is-?"

"The party's fine; I just… wanted to catch my breath," John said, smiling reassuringly at her; he didn't think these people were easily offended, but it was better to be safe than sorry. "We haven't been to many of these things; it's a bit trickier closer to the galactic centre, you know…"

"Indeed," the woman said, smiling slightly at him. "Forgive me, but I had heard that a… Colonel Sumner was the military commander of Atlantis?"

"He moved on from the city," John said, going with the diplomatic explanation they'd come up with; Sumner's attitude at least ensured that he hadn't formed any particular bonds with any of the civilisations they'd encountered over the years, but it was better to be safe rather than sorry. "John Sheppard; I'm the expedition's new director of military operations. You are?"

"I am Ida," the woman said, before her eyes narrowed and her friendly expression vanished. "And your city's false Phantom killed my brother."

Even with his years of training as the Phantom, John was just slightly too slow to react (In hindsight, he'd blame it on the fact that he hadn't been expecting an attack here and he'd been drinking some of the planet's wine lately). Before he could get out of range, Ida had jammed something that felt like a taser into his chest, and he was falling backwards, consciousness fading, mouth open in a weak attempt to call for help…


End file.
